Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017900.1 Corchorus olitorius cultivar O-4 contig17933, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 29162
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:650 original size:331 final size:331
Alignment explanation
Indices: 1--1868 Score: 2176
Period size: 331 Copynumber: 5.6 Consensus size: 331
* * * *
1 AACCATGATGGTTAACGTACATGATTTCGGCTAAAAATTTTGCAAAAATTGACCTGAATTATTTT
1 AACCGTGATGGTT-A-GTACATGATTTCAGCT-AAAATTTTGCAAAAATTGACCCGAAATATTTT
* * **
66 TCCACAATTTTTTTCCCAAAATATGCATAAAAAATATATAATTGAACGCAAAAAAAGATTTGGCG
63 TCCTCAA-TTTTTGCCCAAAATATGCAT-AAAAATATATAATTGAAC-CCCAAAAAGA-TTGGCG
* * * * *
131 GGCTTTTTCACGCTTC-AATTATGGTTTTT-TTATTTTTTTCCAAATTAAGTTCTGATTAAATTG
124 GGC-TTTTCACGCTTCTAA-TATCGTTTTTCCTA-TTTTTTCCAAATTAATTTCCGATTAAATCG
* * * *
194 AAACAAAATTCATATGCTTGTAAAAACATTTCCTTAAATCCAATGTGGCCGAGATTTGATTAGAT
186 AAACAAGATTCAGATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* ***
259 GAATATAGATATTTCAATGAGTCTCTGCGCCAAAAATAATGCAAAACTA-AGTATGAGCCCCGGA
251 GAATATAGATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAAC-AGAGCCGGAGCCCCGGA
323 ACGCGTTTTCAGCCAGA
315 ACGCGTTTTCAGCCAGA
* *
340 AACCGTGATGGTTAACGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTT
1 AACCGTGATGGTT-A-GTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTT
405 CCTCAATTTTTGCCCAAAATATGCAT-AAAATATATAATTGAACCCCAAAAAGATTGGCGGGCTT
64 CCTCAATTTTTGCCCAAAATATGCATAAAAATATATAATTGAACCCCAAAAAGATTGGCGGGCTT
469 TTCACGCTTCTAATATCG-TTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAACAAGA
129 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAACAAGA
* * *
533 TTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCCGAGATTTTATTAGATGAATATAG
194 TTCAGATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG
*
598 ATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCGTTTT
259 ATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCGTTTT
663 CAGCCAGA
324 CAGCCAGA
** ** * *
671 AATTGTGATGAATAGTACATGATTACAGCTAAAATTTTGCAAAAATTGACCCGCAATATTTTTCC
1 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
* * * *
736 TTAATTTTTGCCCAAAATATGCGTAAATAATATATAATTGAACGCCAAAAATATTGGCGGGCTTT
66 TCAATTTTTGCCCAAAATATGCATAAA-AATATATAATTGAACCCCAAAAAGATTGGCGGGCTTT
* **
801 TCACGCTTCTAATATCGTTTTTACTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
130 TCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAACAAGAT
* ** ** * *
866 TTAGATGCTCGTAAAAACATTTTTTTTAAATCCAATAAGGCTGCGAATTGATTAGATGAATATAG
195 TCAGATGCTCGTAAAAACA-TTTCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG
* * * * * * *
931 ATATTTCAAGGAGTCTCTACGCCAAAAATCATGTAAAACTGAGCCGGGGCCCTGGAACGCATTTT
259 ATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCGTTTT
996 CAGCCAGA
324 CAGCCAGA
* * * * * * ***
1004 ACCCTTGTTGGTTAATACACGATTTTCAGCTAAAATTTTG-ATAAAACTGAAATGAAA-AGTTTT
1 AACCGTGATGGTTAGTACATGA-TTTCAGCTAAAATTTTGCA-AAAATTGACCCGAAATA-TTTT
* * * * ** * * * ** ***
1067 TCGTTAATTTTTTGGCCACAGCACT-CATAAAAA-ATATATATTCAA-CTCAAGACTATTTAAGG
63 TCCTCAA-TTTTTGCCCAAAATA-TGCATAAAAATATATA-ATTGAACCCCAAAAAGATTGGCGG
* * * * * * *
1129 GTTTTTCATGCCTCAAATAT-G---TT--T-TTTTTTCGAAATTAATTTCTGATTATATCGAAAC
125 GCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAAC
* * *
1187 AAGATTCTGATGCTCGTAAAAATATTCCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
190 AAGATTCAGATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
*
1252 ATAGATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCG
255 ATAGATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCG
1317 TTTTCAGCCAGA
320 TTTTCAGCCAGA
1329 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
1 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
*
1394 TCAATTTTTGCCCAAAATATGTC-TAAATAATATATAATTGAACGCCAAAAAGATTGGCGGGCTT
66 TCAATTTTTGCCCAAAATATG-CATAAA-AATATATAATTGAACCCCAAAAAGATTGGCGGGCTT
1458 TTCACGCTTCTAATATCGTTTTTACTATTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATC
129 TTCACGCTTCTAATATCG---------TTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATC
* * * *
1523 GAAACAAGATTCAGATGTTCGTAAATACATTTCTTTAAATCCAATGTGGCTAAGATTTGATTAGA
185 GAAACAAGATTCAGATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
* * * *
1588 T-AATTATAGATATTTCAATGAGTCTCTGCACCAAAAATCA-G----TC-GA-----TGCCCCGT
250 TGAA-TATAGATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGG
1641 AACGCGTTTTCAGCCAGA
314 AACGCGTTTTCAGCCAGA
* ** * * * * *
1659 AACCATGATGGTTAGTTTATGATTTCGGCTAAAATTTTACAAAAATTAACCTGAAATAGTTTTCC
1 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
** * ** * *
1724 TCAATTTTCCCCCAAAATATGCATAAAAAATAGATAATTGAATGCCAAAAAGATTGGCAGTCTTT
66 TCAATTTTTGCCCAAAATATGCAT-AAAAATATATAATTGAACCCCAAAAAGATTGGCGGGCTTT
* * *
1789 TCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAAATAATTTCCGATTAAATCAAAATAAGAT
130 TCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAACAAGAT
*
1854 TCAGATGCTCATAAA
195 TCAGATGCTCGTAAA
1869 CATATCCATA
Statistics
Matches: 1318, Mismatches: 172, Indels: 96
0.83 0.11 0.06
Matches are distributed among these distances:
321 58 0.04
322 1 0.00
323 15 0.01
324 45 0.03
325 152 0.12
326 53 0.04
327 1 0.00
329 72 0.05
330 155 0.12
331 229 0.17
332 81 0.06
333 158 0.12
334 51 0.04
335 35 0.03
336 2 0.00
337 19 0.01
338 38 0.03
339 30 0.02
340 4 0.00
341 119 0.09
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (331 bp):
AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
TCAATTTTTGCCCAAAATATGCATAAAAATATATAATTGAACCCCAAAAAGATTGGCGGGCTTTT
CACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
ATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCGTTTTCA
GCCAGA
Found at i:1389 original size:658 final size:659
Alignment explanation
Indices: 1--1880 Score: 2200
Period size: 658 Copynumber: 2.8 Consensus size: 659
* * * *
1 AACCATGATGGTTAACGTACATGATTTCGGCTAAAAATTTTGCAAAAATTGACCTGAATTATTTT
1 AACCGTGATGGTT-A-GTACATGATTTCAGCT-AAAATTTTGCAAAAATTGACCCGAAATATTTT
* * * *
66 TCCACAATTTTTTTCCCAAAATATGCATAAAAAATATATAATTGAACGCAAAAAAAGATTTGGCG
63 TCCTCAA-TTTTTGCCCAAAATATGC-TAAATAATATATAATTGAACGC-CAAAAAGA-TTGGCG
* * * *
131 GGCTTTTTCACGCTTC-AATTATGGTTTTT-TTATTTTTTTCCAAATTAAGTTCTGATTAAATTG
124 GGC-TTTTCACGCTTCTAA-TATCGTTTTTACTA-TTTTTTCCAAATTAATTTCTGATTAAATCG
* * * * *
194 AAACAAAATTCATATGCTTGTAAAAACATTTCCTTAAATCCAATGTGGCCGAGATTTGATTAGAT
186 AAACAAGATTCAGATGCTCGTAAAAACATTTCTTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* * *
259 GAATATAGATATTTCAATGAGTCTCTGCGCCAAAAATAATGCAAAACTAAGTATGAGCCCCGGAA
251 GAATATAGATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACTAAGCAGGAGCCCCGGAA
* * *
324 CGCGTTTTCAGCCAGAAACCGTGATGGTTAACGTACACGATTTCGGCTAAAATTTTGCAAAAATT
316 CGCATTTTCAGCCAGAAACCGTGATGGTTAAC-TACACGATTTCAGCTAAAATTTTGCAAAAACT
** * * *
389 GACCCGAAATATTTTTCCTCAATTTTTGCCCAAAATATGCATAAAATATATAATTGAACCCCAAA
380 GAAACGAAATATTTTTCCTCAATTTTTGCCCAAAACATGCATAAAAAATATAATTCAACCCCAAA
** * *
454 AAGATTGGCGGGCTTTTCACGCTTCTAATATCGTTTTCCTATTTTTTCCAAATTAATTTCCGATT
445 AAGATTGAAGGGCTTTTCACGCCTCAAATATCG-TTT-CTATTTTTTCCAAATTAATTTCCGATT
*
519 AAATCGAAACAAGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCCGAGATTTTA
508 AAATCGAAACAAGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCCGAGATTTGA
584 TTAGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCC
573 TTAGATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCC
649 CCGGAACGCGTTTTCAGCCAGA
638 CCGGAACGCGTTTTCAGCCAGA
** ** * *
671 AATTGTGATGAATAGTACATGATTACAGCTAAAATTTTGCAAAAATTGACCCGCAATATTTTTCC
1 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
* *
736 TTAATTTTTGCCCAAAATATGCGTAAATAATATATAATTGAACGCCAAAAATATTGGCGGGCTTT
66 TCAATTTTTGCCCAAAATATGC-TAAATAATATATAATTGAACGCCAAAAAGATTGGCGGGCTTT
*
801 TCACGCTTCTAATATCGTTTTTACTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
130 TCACGCTTCTAATATCGTTTTTACTATTTTTTCCAAATTAATTTCTGATTAAATCGAAACAAGAT
* * ** * *
866 TTAGATGCTCGTAAAAACATTTTTTTTAAATCCAATAAGGCTGCGAATTGATTAGATGAATATAG
195 TCAGATGCTCGTAAAAACA-TTTCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG
* * * * * * *
931 ATATTTCAAGGAGTCTCTACGCCAAAAATCATGTAAAACTGAGCCGGGGCCCTGGAACGCATTTT
259 ATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACTAAGCAGGAGCCCCGGAACGCATTTT
* * * *
996 CAGCCAGAACCCTTGTTGGTTAA-TACACGATTTTCAGCTAAAATTTTG-ATAAAACTGAAATGA
324 CAGCCAGAAACCGTGATGGTTAACTACACGA-TTTCAGCTAAAATTTTGCA-AAAACTGAAACGA
* * * * * * * **
1059 AA-AGTTTTTCGTTAATTTTTTGGCCACAGCACT-CATAAAAAATATATATTCAA-CTCAAGACT
387 AATA-TTTTTCCTCAA-TTTTTGCCCAAAACA-TGCATAAAAAATATA-ATTCAACCCCAAAAAG
* * * * * *
1121 ATTTAAGGGTTTTTCATGCCTCAAATAT-G-TT-T-TTTTTTCGAAATTAATTTCTGATTATATC
448 ATTGAAGGGCTTTTCACGCCTCAAATATCGTTTCTATTTTTTCCAAATTAATTTCCGATTAAATC
* * *
1182 GAAACAAGATTCTGATGCTCGTAAAAATAT-TCCCTTAAATCCAATGTGGCTGAGATTTGATTAG
513 GAAACAAGATTCAGATGCTCGTAAAAACATAT-CCTTAAATCCAATGTGGCCGAGATTTGATTAG
1246 ATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGG
577 ATGAATATAGATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGG
1311 AACGCGTTTTCAGCCAGA
642 AACGCGTTTTCAGCCAGA
1329 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
1 AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
1394 TCAATTTTTGCCCAAAATATGTCTAAATAATATATAATTGAACGCCAAAAAGATTGGCGGGCTTT
66 TCAATTTTTGCCCAAAATATG-CTAAATAATATATAATTGAACGCCAAAAAGATTGGCGGGCTTT
*
1459 TCACGCTTCTAATATCGTTTTTACTATTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCG
130 TCACGCTTCTAATATCG-TTTT--TA------CTATTTTTTCCAAATTAATTTCTGATTAAATCG
* * *
1524 AAACAAGATTCAGATGTTCGTAAATACATTTCTTTAAATCCAATGTGGCTAAGATTTGATTAGAT
186 AAACAAGATTCAGATGCTCGTAAAAACATTTCTTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* *
1589 -AATTATAGATATTTCAATGAGTCTCTGCACCAAAAATCA-G------T---C--GATGCCCCGT
251 GAA-TATAGATATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACTAAGCAGGA-GCCCCGG
* * * ** * * *
1641 AACGCGTTTTCAGCCAGAAACCATGATGGTT-AGTTTATGATTTCGGCTAAAATTTTACAAAAA-
314 AACGCATTTTCAGCCAGAAACCGTGATGGTTAACTACACGATTTCAGCTAAAATTTTGCAAAAAC
* * * ** * * **
1704 TTAACCTGAAATAGTTTTCCTCAATTTTCCCCCAAAATATGCATAAAAAATAGATAATTGAATGC
379 TGAAAC-GAAATATTTTTCCTCAATTTTTGCCCAAAACATGCATAAAAAAT--ATAATTCAACCC
* * * * *
1769 CAAAAAGATTGGCA-GTCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAAATAATTT
441 CAAAAAGATT-GAAGGGCTTTTCACGCCTCAAATATCG--TTT-CTATTTTTTCCAAATTAATTT
* * * *
1833 CCGATTAAATCAAAATAAGATTCAGATGCTC--ATAAACATATCCATAAA
502 CCGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACATATCCTTAAA
1881 AATATTTTCT
Statistics
Matches: 1024, Mismatches: 147, Indels: 88
0.81 0.12 0.07
Matches are distributed among these distances:
652 1 0.00
653 22 0.02
654 38 0.04
655 64 0.06
656 3 0.00
657 1 0.00
658 304 0.30
659 9 0.01
660 12 0.01
661 6 0.01
662 51 0.05
663 109 0.11
664 174 0.17
665 15 0.01
666 102 0.10
667 90 0.09
668 14 0.01
669 1 0.00
670 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (659 bp):
AACCGTGATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCC
TCAATTTTTGCCCAAAATATGCTAAATAATATATAATTGAACGCCAAAAAGATTGGCGGGCTTTT
CACGCTTCTAATATCGTTTTTACTATTTTTTCCAAATTAATTTCTGATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACATTTCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
ATTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACTAAGCAGGAGCCCCGGAACGCATTTTCA
GCCAGAAACCGTGATGGTTAACTACACGATTTCAGCTAAAATTTTGCAAAAACTGAAACGAAATA
TTTTTCCTCAATTTTTGCCCAAAACATGCATAAAAAATATAATTCAACCCCAAAAAGATTGAAGG
GCTTTTCACGCCTCAAATATCGTTTCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAACAAG
ATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCCGAGATTTGATTAGATGAATATA
GATATTTCAATGAGTCTTTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCGTTT
TCAGCCAGA
Found at i:2132 original size:16 final size:17
Alignment explanation
Indices: 2096--2133 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2086 TTCGGGTTGA
2096 TCGGG-TTCGGATCATT
1 TCGGGTTTCGGATCATT
2112 T-GGGTTTCGG-TCATT
1 TCGGGTTTCGGATCATT
2127 TCGGGTT
1 TCGGGTT
2134 CGGGTCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.08, C:0.16, G:0.34, T:0.42
Consensus pattern (17 bp):
TCGGGTTTCGGATCATT
Found at i:2139 original size:16 final size:16
Alignment explanation
Indices: 2096--2169 Score: 73
Period size: 15 Copynumber: 4.8 Consensus size: 16
2086 TTCGGGTTGA
*
2096 TCGGGTTCGGATCATT
1 TCGGGTTCGGGTCATT
2112 T-GGGTTTC-GGTCATT
1 TCGGG-TTCGGGTCATT
*
2127 TCGGGTTCGGGTCGTT
1 TCGGGTTCGGGTCATT
* * *
2143 T-GGATTCGAGTAATT
1 TCGGGTTCGGGTCATT
2158 TCGGGTTCGGGT
1 TCGGGTTCGGGT
2170 ATCCAAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
15 24 0.52
16 22 0.48
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:2168 original size:31 final size:31
Alignment explanation
Indices: 2096--2169 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2086 TTCGGGTTGA
* * *
2096 TCGGGTTCGGATCATTTGGGTTTCGGTCATT
1 TCGGGTTCGGGTCATTTGGGATTCGGTAATT
*
2127 TCGGGTTCGGGTCGTTT-GGATTCGAGTAATT
1 TCGGGTTCGGGTCATTTGGGATTCG-GTAATT
2158 TCGGGTTCGGGT
1 TCGGGTTCGGGT
2170 ATCCAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39
Consensus pattern (31 bp):
TCGGGTTCGGGTCATTTGGGATTCGGTAATT
Found at i:7258 original size:15 final size:16
Alignment explanation
Indices: 7238--7275 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
7228 CGTTCAAATG
7238 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
7253 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
7270 T-GGGTC
1 TCGGGTC
7276 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:13872 original size:70 final size:68
Alignment explanation
Indices: 13773--14010 Score: 263
Period size: 70 Copynumber: 3.5 Consensus size: 68
13763 AGTAAGGTTT
* * *
13773 TATTCTTC-TTTCCTAAAACACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTTAAACATTCAA
1 TATT-TTCATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTT--GCATTCAA
*
13837 GTGTAG
63 GTTTAG
* *
13843 TATTTTCATTTCCAAAAATATCCTTTCGGTCAAAGGGTCAGTCTCGTCTTTTTTCTGCATTCAAG
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTC-TTTTT-TGCATTCAAG
13908 TTTAG
64 TTTAG
* * * * *
13913 TATTTTTATTTCCAAAAATACCCTTTCAGTCGAAA-GTTCAGT-TTCATC-TTTTTGCATTCAGG
1 TATTTTCATTTCCAAAAATACCCTTTCGGTC-AAAGGGTCAGTCTT-GTCTTTTTTGCATTCAAG
13975 TTTAG
64 TTTAG
*
13980 T-TTTAC-TTTCCAAAAATACCCTTTCGGTCAA
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCAA
14011 GGGCGAGCTT
Statistics
Matches: 147, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
64 2 0.01
65 22 0.15
66 3 0.02
67 15 0.10
68 4 0.03
69 4 0.03
70 88 0.60
71 8 0.05
72 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (68 bp):
TATTTTCATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTTGTCTTTTTTGCATTCAAGTT
TAG
Found at i:15684 original size:23 final size:23
Alignment explanation
Indices: 15653--15699 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
15643 TATGTATTTT
*
15653 GATGGTTGTGATCATACAATGTG
1 GATGGTTGTGATCATACAACGTG
*
15676 GATGTTTGTGATCATACAACGTG
1 GATGGTTGTGATCATACAACGTG
15699 G
1 G
15700 GTGGCTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.34
Consensus pattern (23 bp):
GATGGTTGTGATCATACAACGTG
Found at i:16555 original size:42 final size:42
Alignment explanation
Indices: 16501--16582 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
16491 AAATTCTAGG
*
16501 ACTCCACCTCTAGGTAATTCATCAAAATAAAGCTAATATTCT
1 ACTCCACCTCTAGATAATTCATCAAAATAAAGCTAATATTCT
*
16543 ACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 ACTCCACCTCTAGATAATTCATCAAAATAAAGCTAATATT
16583 AATTGTTGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (42 bp):
ACTCCACCTCTAGATAATTCATCAAAATAAAGCTAATATTCT
Found at i:25726 original size:66 final size:66
Alignment explanation
Indices: 25656--25792 Score: 202
Period size: 66 Copynumber: 2.1 Consensus size: 66
25646 GGCTAAGGAT
* * * *
25656 GCAAAAGATACTACAGTGGAAAAGGCGTCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCA
1 GCAAAAGACACAACAATGGAAAAGGCGGCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCA
25721 A
66 A
* * * *
25722 GCAAAGGACGCAACAATGGATAAGGCGGCAGAGTATGGCAATTATGCAGCCGACAAAGCTAGGCA
1 GCAAAAGACACAACAATGGAAAAGGCGGCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCA
25787 A
66 A
25788 GCAAA
1 GCAAA
25793 GGATGCAACA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.12
Consensus pattern (66 bp):
GCAAAAGACACAACAATGGAAAAGGCGGCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCA
A
Found at i:25793 original size:66 final size:66
Alignment explanation
Indices: 25672--25802 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
25662 GATACTACAG
*
25672 TGGAAAAGGCGTCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCAAGCAAAGGACGCAACA
1 TGGAAAAGGCGGCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCAAGCAAAGGACGCAACA
25737 A
66 A
* * *
25738 TGGATAAGGCGGCAGAGTATGGCAATTATGCAGCCGACAAAGCTAGGCAAGCAAAGGATGCAACA
1 TGGAAAAGGCGGCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCAAGCAAAGGACGCAACA
25803 GTTGACACGG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (66 bp):
TGGAAAAGGCGGCAGAGTATGGCAACTATGCAGCCGACAAAGCTAGGCAAGCAAAGGACGCAACA
A
Found at i:25876 original size:33 final size:33
Alignment explanation
Indices: 25839--26032 Score: 221
Period size: 33 Copynumber: 5.9 Consensus size: 33
25829 GAGGGCAAAA
* *
25839 GAAGGGGC-GCAATATGCAGCGGAGAAGACGAGG
1 GAAGGGGCGGC-ATATGCAGGGGAGAAGGCGAGG
* * * *
25872 GAAGGGGCTGCATATACAGGTGAGAAGGCAAGG
1 GAAGGGGCGGCATATGCAGGGGAGAAGGCGAGG
* * *
25905 GAAGGGGCGGCTTATGCAGGGGAGAAGACGAAG
1 GAAGGGGCGGCATATGCAGGGGAGAAGGCGAGG
* *
25938 GAAGGCGC-GCAATATGCAGGGGAGAAGGCGAGA
1 GAAGGGGCGGC-ATATGCAGGGGAGAAGGCGAGG
* *
25971 GAAGGGGCGGCATATACAGGGGAGAAGGCGAGA
1 GAAGGGGCGGCATATGCAGGGGAGAAGGCGAGG
* *
26004 GAAGGAGCGGAATATGCAGGGGAGAAGGC
1 GAAGGGGCGGCATATGCAGGGGAGAAGGC
26033 AAAAGAAGGA
Statistics
Matches: 136, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
32 2 0.01
33 130 0.96
34 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.46, T:0.08
Consensus pattern (33 bp):
GAAGGGGCGGCATATGCAGGGGAGAAGGCGAGG
Found at i:25941 original size:66 final size:65
Alignment explanation
Indices: 25826--26041 Score: 238
Period size: 66 Copynumber: 3.3 Consensus size: 65
25816 AGGGAGCGGC
* * * * * *
25826 GGAGAGGGCAAAAGAAGGGGC-GCAATATGCAGCGGAGAAGACGAGGGAAGGGGCTGCATATACA
1 GGAGAAGGCAAGAGAAGGGGCGGC-ATATGCAGGGGAGAAGACGAAGGAAGGAGC-GCATATGCA
25890 GG
64 GG
* * * *
25892 TGAGAAGGCAAGGGAAGGGGCGGCTTATGCAGGGGAGAAGACGAAGGAAGGCGCGCAATATGCAG
1 GGAGAAGGCAAGAGAAGGGGCGGCATATGCAGGGGAGAAGACGAAGGAAGGAGCGC-ATATGCAG
25957 G
65 G
* * * *
25958 GGAGAAGGCGAGAGAAGGGGCGGCATATACAGGGGAGAAGGCG-AGAGAAGGAGCGGAATATGCA
1 GGAGAAGGCAAGAGAAGGGGCGGCATATGCAGGGGAGAAGACGAAG-GAAGGAGC-GCATATGCA
26022 GG
64 GG
*
26024 GGAGAAGGCAAAAGAAGG
1 GGAGAAGGCAAGAGAAGG
26042 AAAAGATGCA
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
65 4 0.03
66 120 0.94
67 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.46, T:0.07
Consensus pattern (65 bp):
GGAGAAGGCAAGAGAAGGGGCGGCATATGCAGGGGAGAAGACGAAGGAAGGAGCGCATATGCAGG
Found at i:26041 original size:99 final size:99
Alignment explanation
Indices: 25826--26041 Score: 297
Period size: 99 Copynumber: 2.2 Consensus size: 99
25816 AGGGAGCGGC
* * * *
25826 GGAGAGGGCAAAAGAAGGGGCGCAATATGCAGCGGAGAAGACGAGGGAAGGGGCTGCATATACAG
1 GGAGAAGGCAAAAGAAGGCGCGCAATATGCAGCGGAGAAGACGAGAGAAGGGGCGGCATATACAG
* * * **
25891 GTGAGAAGGCAAGGGAAGGGGCGGCTTATGCAGG
66 GGGAGAAGGCAAGAGAAGGAGCGGAATATGCAGG
* * * * *
25925 GGAGAAGACGAAGGAAGGCGCGCAATATGCAGGGGAGAAGGCGAGAGAAGGGGCGGCATATACAG
1 GGAGAAGGCAAAAGAAGGCGCGCAATATGCAGCGGAGAAGACGAGAGAAGGGGCGGCATATACAG
*
25990 GGGAGAAGGCGAGAGAAGGAGCGGAATATGCAGG
66 GGGAGAAGGCAAGAGAAGGAGCGGAATATGCAGG
26024 GGAGAAGGCAAAAGAAGG
1 GGAGAAGGCAAAAGAAGG
26042 AAAAGATGCA
Statistics
Matches: 99, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.35, C:0.12, G:0.46, T:0.07
Consensus pattern (99 bp):
GGAGAAGGCAAAAGAAGGCGCGCAATATGCAGCGGAGAAGACGAGAGAAGGGGCGGCATATACAG
GGGAGAAGGCAAGAGAAGGAGCGGAATATGCAGG
Found at i:26243 original size:33 final size:33
Alignment explanation
Indices: 26131--26221 Score: 182
Period size: 33 Copynumber: 2.8 Consensus size: 33
26121 ACTGGAAAAA
26131 CAGAGGAAACCAAGCAGAAGGCATCGGAAACTG
1 CAGAGGAAACCAAGCAGAAGGCATCGGAAACTG
26164 CAGAGGAAACCAAGCAGAAGGCATCGGAAACTG
1 CAGAGGAAACCAAGCAGAAGGCATCGGAAACTG
26197 CAGAGGAAACCAAGCAGAAGGCATC
1 CAGAGGAAACCAAGCAGAAGGCATC
26222 AGAGACCGCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.43, C:0.22, G:0.30, T:0.05
Consensus pattern (33 bp):
CAGAGGAAACCAAGCAGAAGGCATCGGAAACTG
Found at i:28523 original size:15 final size:15
Alignment explanation
Indices: 28505--28538 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28495 AAACAATAAT
28505 TGAAAATTT-TCTAAA
1 TGAAAATTTATC-AAA
28520 TGAAAATTTATCAAA
1 TGAAAATTTATCAAA
28535 TGAA
1 TGAA
28539 GGAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (15 bp):
TGAAAATTTATCAAA
Found at i:28707 original size:213 final size:213
Alignment explanation
Indices: 28307--28708 Score: 612
Period size: 213 Copynumber: 1.9 Consensus size: 213
28297 GACAATAATA
* *
28307 AAAAATTATCCAATGAAGGAATCCAATGTGATGCTTATCTAGTAAGATTTGAAGTTTGAGTTATA
1 AAAAATTATCAAATGAAGGAATCCAATGTGATGCTTATCTAGTAAAATTTGAAGTTTGAGTTATA
* * * *
28372 TGAATGTAAAAAAAATATAGCATTCGAAGAACTTTCCTCATTCGAGTCTATACGAGTAACACAGC
66 TGAATGT-AAAAAAATATAGCAATCGAAGAACTTTCCTCATTCGAGTCAACACGAGTAACACAAC
* * * * **
28437 TCAATTGTCACATGTATAATGTGATTACCGCAGTTTTGTAAAATGAATTAATTAAAAAAAACAAT
130 TCAATTGTCACACGTATAATGTGACTACCACAGTTTCGTAAAA-GAACGAATTAAAAAAAACAAT
28502 AATTGAAAATTTTCTAAATG
194 AATTGAAAATTTTCTAAATG
*
28522 AAAATTTATCAAATGAAGGAATCCAATGTGATGCTTATCTAGTAAAATTTGAAGTTTGAGTTATA
1 AAAAATTATCAAATGAAGGAATCCAATGTGATGCTTATCTAGTAAAATTTGAAGTTTGAGTTATA
28587 TGAATGT-AAAAAATATAGCAATCGAAGAACTTTCCTCATTCG-GATCAACACGAGTAACACAAC
66 TGAATGTAAAAAAATATAGCAATCGAAGAACTTTCCTCATTCGAG-TCAACACGAGTAACACAAC
* *
28650 TCAATTGTCACACGTATAATGTGACTATCACAGTTTCGTAATAA-AACGAATTTAAAAAA
130 TCAATTGTCACACGTATAATGTGACTACCACAGTTTCGTAA-AAGAACGAATTAAAAAAA
28709 TAAAAAAGAA
Statistics
Matches: 170, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
212 13 0.08
213 86 0.51
214 2 0.01
215 69 0.41
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (213 bp):
AAAAATTATCAAATGAAGGAATCCAATGTGATGCTTATCTAGTAAAATTTGAAGTTTGAGTTATA
TGAATGTAAAAAAATATAGCAATCGAAGAACTTTCCTCATTCGAGTCAACACGAGTAACACAACT
CAATTGTCACACGTATAATGTGACTACCACAGTTTCGTAAAAGAACGAATTAAAAAAAACAATAA
TTGAAAATTTTCTAAATG
Done.